Hey triumph - this article is worth a read and has some very good information.
http://www.telepathictalk.com/article_f ... potty.html" onclick="window.open(this.href);return false;
Cats, as I'm sure you know, are incredibly clean animals so urinating outside the litter box like that is definitely a sign that something's not right. It could be stress due to the change in his environment as he's only been with you a few days, or it could be that he doesn't like the litter facilities, or both!
What sort of litter trays do you have down for the kittens at the moment and what litter are you using? It also sounds silly but make sure you've got enough litter in the tray - depth matters as they like to dig. Rescues and vets often just use a thin layer to cut down on costs but ideally it needs to be a few inches deep to keep them happy. I know you say the trays have been used but it could well be that your male kitten isn't as impressed with the facilities as the female. I'd start by changing his litter facilities. Perhaps keep one tray as it is and change the other for a different style of tray with an entirely different style of litter and see how he gets on.
As for the sofa, unfortunately once a cat starts weeing in a specific place it's very hard to eradicate the smell entirely and stop them from repeating, although using vinegar was definitely a good move. You need to break the cycle with the sofa as soon as possible before it becomes a routine for him. I'd remove the throw entirely, if you haven't already, so he no longer has access to it as despite washing it he'll probably still be able to smell his urine. Put it away in a cupboard or somewhere he can't get to it for now. It'll probably be fine to use in future once he's a little older and past this problem but for now it'd be better to remove it from the equation.
If he still pee'd on the sofa with a waterproof cover on it then it does suggest it's not just the smell but the area he's attracted to. Can you limit his access to the sofa overnight for now? If you've got a room you can confine both kittens in overnight I'd strongly suggest you do that for now. The kitchen is often as good as any as it's easy to clean up any messes and is devoid of furnishings that contain lots of smells (usually) so it helps to ease any sensory overload.
If you can confine both kittens in the kitchen at night with beds, litter trays and food/water this would allow you to break the cycle with the sofa and will encourage him to utilise the tray. Once he gets into a habit with the tray you'll hopefully be OK, it's just a case of working out what litter and what tray he likes and cutting back on any stress he may be suffering from his new start with you.
If for some reason you can't confine the kittens at night then I'd suggest you continue to use the waterproof cover on the sofa (to keep your sofa from being damaged) and put a layer of tin foil across the seat of the sofa as cats really don't like it. That will hopefully keep him off it overnight and again, break the cycle. Do still change his litter facilities though - some cats are just super picky about what they like and there are an awful lot of litter types and trays on the market to try

If the rescue was using a particular brand then perhaps see if you can find out what it was!
Best of luck with him - kittens at his age are fairly adaptable and as you've taken him on with his sister he'll hopefully settle more quickly than an only kitten. Once you get to the bottom of the cause of his behaviour you should be able to get him to change it without too much trouble

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